INTRODUCTION: Assessing the functional state of the brain and predicting recovery after acute brain injury (ABI) remains a major unsolved problem. At present, physicians make predictions using clinical examination, traditional scoring systems, and statistical models, which have significant shortcomings and lack the ability to forecast recovery on an individual basis. METHODS: SeeMe is based on analyzing subtle facial expressions in response to auditory commands (i.e., “open your eyes,” “make a smile”) over time and compares the results to a pre-stimulus baseline. These subtle motions are often not detectable by the naked eye. We enrolled 26 comatose ABI patients and 16 healthy volunteers to test this tool. Command-evoked eye-opening movements were compared to clinical observation and the JFK Coma Recovery Scale-Revised (CRS-R). RESULTS: In our study, 22 of 26 (85%) patients recovered consciousness during hospitalization after ABI. On average, SeeMe detected command-evoked eye opening ∼9 days before clinical assessment using the CRS-R and ∼3 days before blinded human raters who observed the recorded videos using the naked eye.Using the optimally identified decision threshold, SeeMe demonstrated the following performance metrics on ABI patients with no eye opening to command (auditory CRS subscale = 2): sensitivity = 74.1%, specificity = 66.6%, positive predictive value = 16.8%, and negative predictive value = 96.6%. CONCLUSIONS: These findings demonstrate the high predictive performance of SeeMe in assessing consciousness in ABI patients and provide a quantitative tool for studying neural circuits and developing novel therapeutic approaches. SeeMe's ability to detect low-amplitude motor movements opens new avenues for understanding and facilitating recovery of consciousness in patients with ABI.

Inositol 1,4,5-triphosphate receptor type 1 (ITPR1) is an endoplasmic reticulum-bound intracellular inositol triphosphate receptor involved in the regulation of intracellular calcium. Pathogenic variants in ITPR1 are associated with spinocerebellar ataxia (SCA) types 15/16 and 29 and have recently been implicated in a facial microsomia syndrome. In this report, we present a family with three affected individuals found to have a heterozygous missense c.800C > T (predicted p.Thr267Met) who present clinically with a SCA29-like syndrome. All three individuals presented with varying degrees of ataxia, developmental delay, and apparent intellectual disability, as well as craniofacial involvement-an uncommon finding in patients with SCA29. The variant was identified using clinical exome sequencing and validated with Sanger sequencing. It is presumed to be inherited via parental germline mosaicism. We present our findings to provide additional evidence for germline mosaic inheritance of SCA29, as well as to expand the clinical phenotype of the syndrome.

An SLC30A9-associated cerebrorenal syndrome was first reported in consanguineous Bedouin kindred by Perez et al. in 2017. Although the function of the gene has not yet been fully elucidated, it may be implicated in Wnt signaling and nuclear regulation, as well as in cell and mitochondrial zinc regulation. In this research report, we present a female proband with two distinct, inherited autosomal recessive loss-of-function SLC30A9 variants from unrelated parents. To our knowledge, this is the first reported case of a possible SLC30A9-associated cerebrorenal syndrome in a nonconsanguineous family. Furthermore, a limited statistical analysis was conducted to identify possible allele frequency differences between populations. Our findings provide further support for an SLC30A9-associated cerebrorenal syndrome and may help clarify the gene's function through its possible disease association.

Members of a paralogous gene family in which variation in one gene is known to cause disease are eight times more likely to also be associated with human disease. Recent studies have elucidated DHX30 and DDX3X as genes for which pathogenic variant alleles are involved in neurodevelopmental disorders. We hypothesized that variants in paralogous genes encoding members of the DExD/H-box RNA helicase superfamily might also underlie developmental delay and/or intellectual disability (DD and/or ID) disease phenotypes. Here we describe 15 unrelated individuals who have DD and/or ID, central nervous system (CNS) dysfunction, vertebral anomalies, and dysmorphic features and were found to have probably damaging variants in DExD/H-box RNA helicase genes. In addition, these individuals exhibit a variety of other tissue and organ system involvement including ocular, outer ear, hearing, cardiac, and kidney tissues. Five individuals with homozygous (one), compound-heterozygous (two), or de novo (two) missense variants in DHX37 were identified by exome sequencing. We identified ten total individuals with missense variants in three other DDX/DHX paralogs: DHX16 (four individuals), DDX54 (three individuals), and DHX34 (three individuals). Most identified variants are rare, predicted to be damaging, and occur at conserved amino acid residues. Taken together, these 15 individuals implicate the DExD/H-box helicases in both dominantly and recessively inherited neurodevelopmental phenotypes and highlight the potential for more than one disease mechanism underlying these disorders.

N-alpha-acetylation is one of the most common co-translational protein modifications in humans and is essential for normal cell function. NAA10 encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. The auxiliary and regulatory subunits of the NatA complex are NAA15 and Huntington-interacting protein (HYPK), respectively. Through a genotype-first approach with exome sequencing, we identified and phenotypically characterized 30 individuals from 30 unrelated families with 17 different de novo or inherited, dominantly acting missense variants in NAA10 or NAA15. Clinical features of affected individuals include variable levels of intellectual disability, delayed speech and motor milestones and autism spectrum disorder. Additionally, some subjects present with mild craniofacial dysmorphology, congenital cardiac anomalies and seizures. One of the individuals is an 11-year-old boy with a frameshift variant in exon 7 of NAA10, who presents most notably with microphthalmia, which confirms a prior finding with a single family with Lenz microphthalmia syndrome. Biochemical analyses of variants as part of the human NatA complex, as well as enzymatic analyses with and without the HYPK regulatory subunit, help to explain some of the phenotypic differences seen among the different variants.

We recently described a new neurodevelopmental syndrome (TAF1/MRXS33 intellectual disability [ID] syndrome) (MIM# 300966) caused by pathogenic variants involving the X-linked gene TATA-box binding protein associated factor 1 (TAF1), which participates in RNA polymerase II transcription. The initial study reported 11 families, and the syndrome was defined as presenting early in life with hypotonia, facial dysmorphia, and developmental delay that evolved into ID and/or autism spectrum disorder. We have now identified an additional 27 families through a genotype-first approach. Familial segregation analysis, clinical phenotyping, and bioinformatics were capitalized on to assess potential variant pathogenicity, and molecular modeling was performed for those variants falling within structurally characterized domains of TAF1. A novel phenotypic clustering approach was also applied, in which the phenotypes of affected individuals were classified using 51 standardized Human Phenotype Ontology terms. Phenotypes associated with TAF1 variants show considerable pleiotropy and clinical variability, but prominent among previously unreported effects were brain morphological abnormalities, seizures, hearing loss, and heart malformations. Our allelic series broadens the phenotypic spectrum of the TAF1/MRXS33 ID syndrome and the range of TAF1 molecular defects in humans. It also illustrates the challenges for determining the pathogenicity of inherited missense variants, particularly for a gene mapping to chromosome X.

N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.

KBG syndrome is a rare autosomal dominant genetic condition characterized by neurological involvement, macrodontia and distinct facial, hand and skeletal features. Over 70 cases have been reported; however it is likely that KBG syndrome is underdiagnosed due to lack of comprehensive characterization of the heterogeneous phenotypic features. We describe the clinical manifestations in a male currently at 13 years of age, who exhibited symptoms including epilepsy, severe developmental delay, distinct facial features and hand anomalies, without positive genetic diagnosis. Subsequent exome sequencing identified a novel de novo heterozygous single base pair insertion (c.6015dupA) in ANKRD11, which was validated by Sanger sequencing. This insertion is predicted to lead to a premature stop codon and loss of function in ANKRD11, thereby implicating it as contributing to the proband’s symptoms and yielding a molecular diagnosis of KBG syndrome for the case. INTRODUCTION Whole exome sequencing (WES) is a method that sequences only regions of the genome that code for proteins and is more comprehensive than other testing methods such as microarray and CNV analyses. WES is useful for detecting disease-contributing variants in genes associated with rare genetic syndromes. Here we report our efforts in phenotypic characterization and molecular diagnosis of a previously undiagnosed pediatric patient. This case demonstrates the utility of whole exome sequencing for finding rare disease-contributing mutations that can then lead to the diagnosis of rare, previously unrecognized syndromes. In this case, we report in a single family the identification of a de novo mutation in ANKRD11, which led to the recognition of KBG syndrome in the sequenced proband. RESULTS Clinical presentation and family history The proband was born to a non-consanguineous couple, who had an unremarkable pregnancy history; however, at birth a large fontanel was reported. Parents and siblings were healthy and no significant family history was reported (Figure 1). The proband had his first epileptic episode at three years of age. After this episode, he lost all speech, began exhibiting autistic behavior, and also started to have frequent generalized tonic-clonic seizures. Over time, tonic, atonic, mild clonic, complex partial, myoclonic and gelastic seizures were reported in the proband. Other developmental skills, including throwing a ball, responding to his name, feeding himself with utensils and self-care skills were lost by 4-years of age. No significant conductive hearing loss, heart abnormalities or delayed bone age were found in the proband at that age. The proband was evaluated (by G.J.L.) at eleven years of age. He presented with several neurological and craniofacial abnormalities including epilepsy, ventriculomegaly, relative macrocephaly, prominent forehead, low hairline, thick eyebrows, wide-set eyes (Figure 2), macrodontia of upper central incisors, and full lips (Figure 3). Hand and foot abnormalities included clinodactyly of the fifth digit, bilateral single transverse palmar creases, brachydactyly (Figure 4) and flat feet. He also had a diagnosis of cerebral folate deficiency due to the presence of folate receptor autoantibodies. Genomic Analyses Blood and saliva samples from the proband as well as his parents and siblings were used as samples to be sequenced. These samples were sent to Affiliated Genetics in Salt Lake City, Utah, where genomic DNA was extracted and exons sequenced using the Life Technologies Ampliseq Exome RDY kit and the Life Technologies Proton sequencing system (see Methods). These targeted regions were sequenced using the Ion Proton sequencing system using Ion Hi-Q Chemistry with 200 bp reads. The DNA sequencing data was compared to the UCSC hg19 reference sequence using several methods of analysis (see Methods). These analyses included in-house protocols and several commercial software packages including Tute Genomics, Omicia Opal, and Cartagenia v4.1, along with the use of an OTG-SNP Caller pipeline (see Methods). The various analyses helped to provide a more comprehensive and in-depth approach to the data . As one example, for the OTG-SNP Caller pipeline, for each individual, the final VCF file contained 20,000 to 25,000 variants, of which around 300-400 variants were found to be autosomal recessive, i.e. heterozygous in both parents, and homozygous only in the proband. However, over a thousand variants were recognized as de novo, which is notably above the expected number of de novo mutations found in WES . Therefore, even with an optimized variant calling pipeline, there were still a significant number of false positives called. Autosomal variants were examined, and there was no evidence found to support any of them as possible contributing mutations. These variants are provided in supplementary files (as described in Methods). For the de novo mutations, a single base insertion of adenine (A) at position 6015 in exon 10 of ANKRD11 (c.6015dupA , p.Gly2006Argfs*26) (Figure 5) was identified as the most relevant mutation. All phenotypic analysis software, including Phenolyzer, wAnnovar, and PhenIX indicated that a heterozygous frame-shift mutation in ANKRD11, or the Ankyrin Repeat Domain 11 gene, might be a contributing factor in this individual’s disease The presence of the mutation was confirmed using Sanger sequencing (Figure 5).This mutation has a CADD score of 32, and is considered to be ‘Deleterious’ by SIFT with a confidence score of 0.858, and is therefore predicted to have a severe effect on protein structure. Although insertions have not yet been reported, other mutations in this gene have been previously identified as contributing to KBG syndrome, a rare disease that affects around 60-70 people worldwide. DISCUSSION Many syndromes affecting neurological development present with heterogeneous and non-distinct phenotypes and therefore remain undiagnosed or are misdiagnosed. The combination of whole exome sequencing combined with detailed and standardized phenotypic documentation is a powerful method to achieve accurate diagnosis. KBG syndrome (OMIM #148050) is a rare, but increasingly recognized, autosomal dominant genetic condition. It was first described in 1975, and is characterized by craniofacial features, hand abnormalities, macrodontia, and neurological involvement including developmental delay and epilepsy. The syndrome’s name was derived from the last names of the first three families found to have this syndrome. Over 70 cases have been reported, however it is likely that KBG syndrome is underdiagnosed due to the fact that dysmorphic features may be subtle and cognitive delay can vary from mild to moderate. Skjei et al. suggested that a clinical diagnosis of KBG syndrome can be made if the individual meets four out of the following eight major criteria: characteristic facial features, macrodontia of upper central incisors, short stature, delayed bone age, neurological involvement, hand abnormalities, costovertebral anomalies and the presence of a family member affected with the syndrome. Facial features include hypertelorism, short nose with broad base and bulbous nasal tip, and broad bushy eyebrows. Although the shape of the face is often described as being round, it has been noted that the shape evolves as affected children develop. Hand abnormalities typically include brachydactyly, clinodactyly of the fifth digit, small hands and nail anomalies. Skeletal anomalies frequently involve the pelvis, thorax, limbs and skull with abnormal curvature of the spine, including kyphosis and scoliosis, being reported in some cases. Minor features of KBG syndrome include cutaneous syndactyly, conductive hearing loss, palatal abnormalities, cryptorchidism, webbed/short neck, strabismus and congenital heart defects. There is some phenotypic overlap with Cornelia de Lange syndrome (CdLS) . Individuals with KBG syndrome have been found to have heterozygous mutations leading to haploinsufficiency of the ankyrin repeat domain 11 (ANKRD11) gene or a 16q24 microdeletion that encompasses ANKRD11. When mutations in the gene affect the highly conserved region of the domain for transcriptional regression, they are predicted to lead to premature stop codons which could result in haploinsufficiency and when a 16q24 microdeletion is present the haploinsufficency of ANKRD11 is confirmed to be the pathogenic mechanism of KBG syndrome. Sporadic and familial cases of KBG syndrome have been reported, with familial cases following an autosomal dominant inheritance pattern 15; . ANKRD11 (ankyrin repeat domain containing protein 11) is a chromatin regulator that controls histone acetylation and gene expression during neural development. There are two functional domains that act as transcriptional repressors and one domain that functions as a transcriptional promoter. The majority of reported mutations in KBG syndrome result in a truncated protein that affects a domain for transcriptional repression. ANKRD11 interacts with the p160 coactivator and the nuclear receptor complex and it functions to inhibit ligand-dependent transcriptional activation by recruiting histone deacytelases (HDACs). Additionally, ANKRD11 was also found to play a role in enhancing the transcriptional activity of p53. Homozygosity for a missense mutation in ANKRD11 is embryonic lethal in mice, whereas the heterozygous mice have an osteopenia-like phenotype and craniofacial abnormalities. This sporadic case of KBG syndrome demonstrates the importance of ongoing investigations of rare conditions. Each case reported in the literature will help to delineate the phenotype so that we may better identify cases in the future and determine appropriate recommendations for clinical management. Current recommendations for management of KBG syndrome include hearing tests, ophthalmologic assessments, echocardiography, an EEG, orthodontic evaluation and skeletal investigation wit

KBG syndrome is a rare autosomal dominant genetic condition characterized by neurological involvement and distinct facial, hand, and skeletal features. More than 70 cases have been reported; however, it is likely that KBG syndrome is underdiagnosed because of lack of comprehensive characterization of the heterogeneous phenotypic features. We describe the clinical manifestations in a male currently 13 years of age, who exhibited symptoms including epilepsy, severe developmental delay, distinct facial features, and hand anomalies, without a positive genetic diagnosis. Subsequent exome sequencing identified a novel de novo heterozygous single base pair duplication (c.6015dupA) in ANKRD11, which was validated by Sanger sequencing. This single-nucleotide duplication is predicted to lead to a premature stop codon and loss of function in ANKRD11, thereby implicating it as contributing to the proband's symptoms and yielding a molecular diagnosis of KBG syndrome. Before molecular diagnosis, this syndrome was not recognized in the proband, as several key features of the disorder were mild and were not recognized by clinicians, further supporting the concept of variable expressivity in many disorders. Although a diagnosis of cerebral folate deficiency has also been given, its significance for the proband's condition remains uncertain.

The SCN8A gene encodes the sodium voltage-gated channel alpha subunit 8. Mutations in this gene have been associated with early infantile epileptic encephalopathy type 13. With the use of whole-exome sequencing, a de novo missense mutation in SCN8A was identified in a 4-yr-old female who initially exhibited symptoms of epilepsy at the age of 5 mo that progressed to a severe condition with very little movement, including being unable to sit or walk on her own.